To change the "Fixed Aspect Ratio" do the following: Open up the Project Pane. Click on the Media tab. Select the AI file. Click on the Inspector tab in the Inspector. Select the Media tab if it is not already selected. Un check the Fixed Resolution check box. Jaggy edges become smooth.

Be sure your Illustrator file is RGB.

By the way, you can not work with the individual layers in a multi layered AI file in Motion. You can do it in AE. To work with multi layers you need to convert the AI to a PSD. Hope this helps and best of luck.